Research output: Contribution to journal › Review article › peer-review
FISH Going Meso-Scale : A Microscopic Search for Chromatin Domains. / Maslova, Antonina; Krasikova, Alla.
In: Frontiers in Cell and Developmental Biology, Vol. 9, 753097, 03.11.2021.Research output: Contribution to journal › Review article › peer-review
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TY - JOUR
T1 - FISH Going Meso-Scale
T2 - A Microscopic Search for Chromatin Domains
AU - Maslova, Antonina
AU - Krasikova, Alla
N1 - Publisher Copyright: © Copyright © 2021 Maslova and Krasikova.
PY - 2021/11/3
Y1 - 2021/11/3
N2 - The intimate relationships between genome structure and function direct efforts toward deciphering three-dimensional chromatin organization within the interphase nuclei at different genomic length scales. For decades, major insights into chromatin structure at the level of large-scale euchromatin and heterochromatin compartments, chromosome territories, and subchromosomal regions resulted from the evolution of light microscopy and fluorescence in situ hybridization. Studies of nanoscale nucleosomal chromatin organization benefited from a variety of electron microscopy techniques. Recent breakthroughs in the investigation of mesoscale chromatin structures have emerged from chromatin conformation capture methods (C-methods). Chromatin has been found to form hierarchical domains with high frequency of local interactions from loop domains to topologically associating domains and compartments. During the last decade, advances in super-resolution light microscopy made these levels of chromatin folding amenable for microscopic examination. Here we are reviewing recent developments in FISH-based approaches for detection, quantitative measurements, and validation of contact chromatin domains deduced from C-based data. We specifically focus on the design and application of Oligopaint probes, which marked the latest progress in the imaging of chromatin domains. Vivid examples of chromatin domain FISH-visualization by means of conventional, super-resolution light and electron microscopy in different model organisms are provided.
AB - The intimate relationships between genome structure and function direct efforts toward deciphering three-dimensional chromatin organization within the interphase nuclei at different genomic length scales. For decades, major insights into chromatin structure at the level of large-scale euchromatin and heterochromatin compartments, chromosome territories, and subchromosomal regions resulted from the evolution of light microscopy and fluorescence in situ hybridization. Studies of nanoscale nucleosomal chromatin organization benefited from a variety of electron microscopy techniques. Recent breakthroughs in the investigation of mesoscale chromatin structures have emerged from chromatin conformation capture methods (C-methods). Chromatin has been found to form hierarchical domains with high frequency of local interactions from loop domains to topologically associating domains and compartments. During the last decade, advances in super-resolution light microscopy made these levels of chromatin folding amenable for microscopic examination. Here we are reviewing recent developments in FISH-based approaches for detection, quantitative measurements, and validation of contact chromatin domains deduced from C-based data. We specifically focus on the design and application of Oligopaint probes, which marked the latest progress in the imaging of chromatin domains. Vivid examples of chromatin domain FISH-visualization by means of conventional, super-resolution light and electron microscopy in different model organisms are provided.
KW - chromatin domains
KW - chromatin imaging
KW - FISH probes
KW - fluorescence in situ hybridization (FISH)
KW - fluorescent microscopy
KW - genome compartments
KW - Oligopaints
KW - topologically associating domains
KW - OLIGONUCLEOTIDE PROBES
KW - MOLECULE-LABELED NUCLEOTIDES
KW - 3D GENOME ARCHITECTURE
KW - IN-SITU HYBRIDIZATION
KW - COMPUTATIONAL METHODS
KW - INTERPHASE CHROMOSOMES
KW - HI-C
KW - DNA PROBES
KW - CHROMOSOME CONFORMATION CAPTURE
KW - 3-DIMENSIONAL ORGANIZATION
UR - http://www.scopus.com/inward/record.url?scp=85119407595&partnerID=8YFLogxK
UR - https://www.mendeley.com/catalogue/129e60ba-5b4b-3904-b85a-981ee7dd8072/
U2 - 10.3389/fcell.2021.753097
DO - 10.3389/fcell.2021.753097
M3 - Review article
AN - SCOPUS:85119407595
VL - 9
JO - Frontiers in Cell and Developmental Biology
JF - Frontiers in Cell and Developmental Biology
SN - 2296-634X
M1 - 753097
ER -
ID: 88907241